Function calculates the distribution of genetic distances in a population of viruses with the given parameters
gendist_distribution(
mut_rate,
mean_gens_pdf,
max_link_gens = 1,
max_gens = NULL,
max_dist = NULL
)mean number of mutations per generation, assumed to be Poisson distributed
the density distribution of the mean number of generations between cases; the index of this vector is assumed to be the discrete distance between cases
the maximum generations of separation for linked pairs
the maximum number of generations to consider, if NULL (default) value is set to the highest
number of generations in mean_gens_pdf with a non-zero probability
the maximum distance to calculate, if NULL (default) value is set to max_gens * 99.9th percentile
of mut_rate Poisson distribution
a data frame with distances and probabilities
Other genetic distance functions:
gendist_roc_format(),
gendist_sensspec_cutoff()
# ebola-like pathogen
R <- 1.5
mut_rate <- 1
# use simulated generation distributions from the provided 'genDistSim' data object
data('genDistSim')
mean_gens_pdf <- as.numeric(genDistSim[genDistSim$R == R, -(1:2)])
# get theoretical genetic distance dist based on mutation rate and generation parameters
gendist_distribution(mut_rate = mut_rate,
mean_gens_pdf = mean_gens_pdf,
max_link_gens = 1)
#> dist linked_prob unlinked_prob
#> [1,] 0 3.678794e-01 7.090339e-04
#> [2,] 1 3.678794e-01 2.120973e-03
#> [3,] 2 1.839397e-01 3.810662e-03
#> [4,] 3 6.131324e-02 5.612427e-03
#> [5,] 4 1.532831e-02 7.590688e-03
#> [6,] 5 3.065662e-03 9.833909e-03
#> [7,] 6 5.109437e-04 1.238470e-02
#> [8,] 7 7.299195e-05 1.524673e-02
#> [9,] 8 9.123994e-06 1.839695e-02
#> [10,] 9 1.013777e-06 2.178995e-02
#> [11,] 10 1.013777e-07 2.535940e-02
#> [12,] 11 9.216156e-09 2.902012e-02
#> [13,] 12 7.680130e-10 3.267160e-02
#> [14,] 13 5.907792e-11 3.620293e-02
#> [15,] 14 4.219851e-12 3.949867e-02
#> [16,] 15 2.813234e-13 4.244516e-02
#> [17,] 16 1.758271e-14 4.493683e-02
#> [18,] 17 1.034277e-15 4.688211e-02
#> [19,] 18 5.745985e-17 4.820856e-02
#> [20,] 19 3.024203e-18 4.886693e-02
#> [21,] 20 1.512101e-19 4.883396e-02
#> [22,] 21 7.200483e-21 4.811368e-02
#> [23,] 22 3.272947e-22 4.673709e-02
#> [24,] 23 1.423020e-23 4.476029e-02
#> [25,] 24 5.929251e-25 4.226109e-02
#> [26,] 25 2.371700e-26 3.933435e-02
#> [27,] 26 9.121925e-28 3.608642e-02
#> [28,] 27 3.378491e-29 3.262913e-02
#> [29,] 28 1.206604e-30 2.907367e-02
#> [30,] 29 4.160703e-32 2.552495e-02
#> [31,] 30 1.386901e-33 2.207678e-02
#> [32,] 31 4.473874e-35 1.880814e-02
#> [33,] 32 1.398086e-36 1.578079e-02
#> [34,] 33 4.236623e-38 1.303827e-02
#> [35,] 34 1.246066e-39 1.060613e-02
#> [36,] 35 3.560187e-41 8.493426e-03
#> [37,] 36 9.889410e-43 6.694922e-03
#> [38,] 37 2.672813e-44 5.193965e-03
#> [39,] 38 7.033720e-46 3.965563e-03
#> [40,] 39 1.803518e-47 2.979420e-03
#> [41,] 40 4.508795e-49 2.202706e-03
#> [42,] 41 1.099706e-50 1.602374e-03
#> [43,] 42 2.618348e-52 1.146955e-03
#> [44,] 43 6.089180e-54 8.078007e-04
#> [45,] 44 1.383905e-55 5.598156e-04
#> [46,] 45 3.075344e-57 3.817538e-04
#> [47,] 46 6.685530e-59 2.561771e-04
#> [48,] 47 1.422453e-60 1.691776e-04
#> [49,] 48 2.963444e-62 1.099572e-04
#> [50,] 49 6.047845e-64 7.034279e-05
#> [51,] 50 1.209569e-65 4.429686e-05
#> [52,] 51 2.371704e-67 2.746180e-05
#> [53,] 52 4.560969e-69 1.676242e-05
#> [54,] 53 8.605602e-71 1.007507e-05
#> [55,] 54 1.593630e-72 5.963713e-06
#> [56,] 55 2.897509e-74 3.476958e-06
#> [57,] 56 5.174123e-76 1.996890e-06
#> [58,] 57 9.077409e-78 1.129900e-06
#> [59,] 58 1.565071e-79 6.299665e-07
#> [60,] 59 2.652662e-81 3.461366e-07
#> [61,] 60 4.421103e-83 1.874529e-07
#> [62,] 61 7.247710e-85 1.000721e-07
#> [63,] 62 1.168986e-86 5.267117e-08
#> [64,] 63 1.855533e-88 2.733592e-08
#> [65,] 64 2.899270e-90 1.399128e-08
#> [66,] 65 4.460415e-92 7.063281e-09
#> [67,] 66 6.758204e-94 3.517564e-09
#> [68,] 67 1.008687e-95 1.728324e-09
#> [69,] 68 1.483364e-97 8.379472e-10
#> [70,] 69 2.149802e-99 4.009374e-10
#> [71,] 70 3.071146e-101 1.893496e-10
#> [72,] 71 4.325558e-103 8.827521e-11
#> [73,] 72 6.007719e-105 4.063104e-11
#> [74,] 73 8.229753e-107 1.846628e-11
#> [75,] 74 1.112129e-108 8.288191e-12
#> [76,] 75 1.482838e-110 3.674133e-12
#> [77,] 76 1.951103e-112 1.608867e-12
#> [78,] 77 2.533900e-114 6.960005e-13
#> [79,] 78 3.248590e-116 2.974932e-13
#> [80,] 79 4.112139e-118 1.256537e-13
#> [81,] 80 5.140174e-120 5.245135e-14
#> [82,] 81 6.345893e-122 2.164074e-14
#> [83,] 82 7.738894e-124 8.826172e-15
#> [84,] 83 9.323969e-126 3.558829e-15
#> [85,] 84 1.109996e-127 1.418813e-15
#> [86,] 85 1.305878e-129 5.593391e-16
#> [87,] 86 1.518463e-131 2.180742e-16
#> [88,] 87 1.745360e-133 8.409295e-17
#> [89,] 88 1.983363e-135 3.207649e-17
#> [90,] 89 2.228498e-137 1.210407e-17
#> [91,] 90 2.476109e-139 4.518956e-18
#> [92,] 91 2.720999e-141 1.669362e-18
#> [93,] 92 2.957607e-143 6.102565e-19
#> [94,] 93 3.180223e-145 2.207832e-19
#> [95,] 94 3.383216e-147 7.905933e-20
#> [96,] 95 3.561280e-149 2.802304e-20
#> [97,] 96 3.709666e-151 9.833158e-21
#> [98,] 97 3.824398e-153 3.416066e-21
#> [99,] 98 3.902447e-155 1.175045e-21
#> [100,] 99 3.941866e-157 4.002361e-22
#> [101,] 100 3.941866e-159 1.350050e-22
#> [102,] 101 3.902838e-161 4.510172e-23
#> [103,] 102 3.826311e-163 1.492391e-23
#> [104,] 103 3.714865e-165 4.891647e-24
#> [105,] 104 3.571986e-167 1.588351e-24
#> [106,] 105 3.401891e-169 5.109656e-25
#> [107,] 106 3.209332e-171 1.628643e-25
#> [108,] 107 2.999375e-173 5.143790e-26
#> [109,] 108 2.777199e-175 1.609895e-26
#> [110,] 109 2.547889e-177 4.993466e-27
#> [111,] 110 2.316263e-179 1.535075e-27
#> [112,] 111 2.086723e-181 4.677484e-28
#> [113,] 112 1.863146e-183 1.412804e-28
#> [114,] 113 1.648802e-185 4.230289e-29
#> [115,] 114 1.446317e-187 1.255762e-29
#> [116,] 115 1.257667e-189 3.695934e-30
#> [117,] 116 1.084196e-191 1.078576e-30
#> [118,] 117 9.266631e-194 3.121161e-31
#> [119,] 118 7.853077e-196 8.956737e-32
#> [120,] 119 6.599225e-198 2.549062e-32
#> [121,] 120 5.499354e-200 7.195089e-33
#> [122,] 121 4.544921e-202 2.014396e-33
#> [123,] 122 3.725345e-204 5.594150e-34
#> [124,] 123 3.028736e-206 1.541100e-34
#> [125,] 124 2.442529e-208 4.211744e-35
#> [126,] 125 1.954023e-210 1.141967e-35
#> [127,] 126 1.550812e-212 3.072074e-36
#> [128,] 127 1.221112e-214 8.200150e-37
#> [129,] 128 9.539935e-217 2.171948e-37
#> [130,] 129 7.395299e-219 5.708725e-38
#> [131,] 130 5.688691e-221 1.489072e-38
#> [132,] 131 4.342512e-223 3.854812e-39
#> [133,] 132 3.289782e-225 9.904341e-40
#> [134,] 133 2.473520e-227 2.525843e-40
#> [135,] 134 1.845911e-229 6.393945e-41
#> [136,] 135 1.367341e-231 1.606704e-41
#> [137,] 136 1.005398e-233 4.008023e-42
#> [138,] 137 7.338672e-236 9.925992e-43
#> [139,] 138 5.317878e-238 2.440559e-43
#> [140,] 139 3.825811e-240 5.957964e-44
#> [141,] 140 2.732722e-242 1.444180e-44
#> [142,] 141 1.938101e-244 3.476005e-45
#> [143,] 142 1.364860e-246 8.308000e-46
#> [144,] 143 9.544475e-249 1.971923e-46
#> [145,] 144 6.628107e-251 4.648162e-47
#> [146,] 145 4.571109e-253 1.088154e-47
#> [147,] 146 3.130896e-255 2.530098e-48
#> [148,] 147 2.129861e-257 5.843076e-49
#> [149,] 148 1.439096e-259 1.340363e-49
#> [150,] 149 9.658359e-262 3.054212e-50
#> [151,] 150 6.438906e-264 6.913382e-51
#> [152,] 151 4.264176e-266 1.554588e-51
#> [153,] 152 2.805379e-268 3.472894e-52
#> [154,] 153 1.833581e-270 7.707930e-53
#> [155,] 154 1.190637e-272 1.699698e-53
#> [156,] 155 7.681530e-275 3.724015e-54
#> [157,] 156 4.924058e-277 8.107262e-55
#> [158,] 157 3.136342e-279 1.753789e-55
#> [159,] 158 1.985027e-281 3.769971e-56
#> [160,] 159 1.248445e-283 8.053285e-57
#> [161,] 160 7.802778e-286 1.709619e-57
#> [162,] 161 4.846446e-288 3.606891e-58
#> [163,] 162 2.991633e-290 7.562942e-59
#> [164,] 163 1.835358e-292 1.576117e-59
#> [165,] 164 1.119121e-294 3.264693e-60
#> [166,] 165 6.782550e-297 6.721526e-61
#> [167,] 166 4.085873e-299 1.375564e-61
#> [168,] 167 2.446631e-301 2.798312e-62
#> [169,] 168 1.456328e-303 5.658868e-63
#> [170,] 169 8.617324e-306 1.137617e-63
#> [171,] 170 5.069014e-308 2.273580e-64